Genetic effects of stearoyl-coenzyme A desaturase (SCD) polymorphism on milk production traits in the Chinese dairy population.

Stearoyl-CoA desaturase (SCD) is a multifunctional complex enzyme important in the cellular biosynthesis of fatty acids. The present study was to investigate the association of the SCD gene with milk production traits in dairy cattle. Two single nucleotide polymorphisms (SNPs) (g.6926A>G and g.8646A>G) in introns 3 and 4, and three SNPs (g.10153A>G, g.10213T>C and g.10329C>T) in exon 5 were identified with pooled DNA sequencing and genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry assay in 752 Chinese Holstein cows. Polymorphism g.10329C>T was predicted to result in an amino acid replacement from alanine to valine in the SCD protein. With a mixed animal model, the significant associations of the five SNPs with 305-day milk, fat and protein yields and protein percentage were determined. We further demonstrated cows with heterozygous genotypes (A/G or C/T) had highest 305 day milk yield, fat yield, protein yield and lowest protein percentage. Heterozygous cows with genotype AG at the g.6926A>G locus showed the greatest milk yield (P < 0.0001), fat yield (P < 0.0001) and protein yield (P < 0.0001) among other heterozygous genotypes at any of the loci. Dominance effects of all identified SNPs on milk, fat and protein yields and protein percentage were significant. Moreover, significant allele substitution effects at g.6926A>G locus on milk yield and at g.10213T>C on protein yield were observed. Five-locus haplotypes and strong linkage disequilibrium (D' > 0.9) between the five SNPs were also observed. The results suggest that identified polymorphisms could be potential genetic markers to improve the production performance of Chinese Holstein.

Alim MA ，Fan YP ，Wu XP ，Xie Y ，Zhang Y ，Zhang SL ，Sun DX ，Zhang Y ，Zhang Q ，Liu L ，Guo G ... -  《-》

A post-GWAS confirming the SCD gene associated with milk medium- and long-chain unsaturated fatty acids in Chinese Holstein population.

The stearoyl-CoA desaturase (delta-9-desaturase) gene encodes a key enzyme in the cellular biosynthesis of monounsaturated fatty acids. In our initial genome-wide association study (GWAS) of Chinese Holstein cows, 19 SNPs fell in a 1.8-Mb region (20.3-22.1 Mb) on chromosome 26 underlying the SCD gene and were highly significantly associated with C14:1 or C14 index. The aims of this study were to verify whether the SCD gene has significant genetic effects on milk fatty acid composition in dairy cattle. By resequencing the entire coding region of the bovine SCD gene, a total of six variations were identified, including three coding variations (g.10153G>A, g.10213T>C and g.10329C>T) and three intronic variations (g.6926A>G, g.8646G>A and g.16158G>C). The SNP in exon 3, g.10329C>T, was predicted to result in an amino acid replacement from alanine (GCG) to valine (GTG) in the SCD protein. An association study for 16 milk fatty acids using 346 Chinese Holstein cows with accurate phenotypes and genotypes was performed using the mixed animal model with the proc mixed procedure in sas 9.2. All six detected SNPs were revealed to be associated with six medium- and long-chain unsaturated fatty acids (P = 0.0457 to P < 0.0001), specifically for C14:1 and C14 index (P = 0.0005 to P < 0.0001). Subsequently, strong linkage disequilibrium (D' = 0.88-1.00) was observed among all six SNPs in SCD and the five SNPs (rs41623887, rs109923480, rs42090224, rs42092174 and rs42091426) within the 1.8-Mb region identified in our previous GWAS, indicating that the significant association of the SCD gene with milk fatty acid content traits reduced the observed significant 1.8-Mb chromosome region in GWAS. Haplotype-based analysis revealed significant associations of the haplotypes encompassing the six SCD SNPs and one SNP (rs109923480) in a GWAS with C14:1, C14 index, C16:1 and C16 index (P = 0.0011 to P < 0.0001). In summary, our findings provide replicate evidence for our previous GWAS and demonstrate that variants in the SCD gene are significantly associated with milk fatty acid composition in dairy cattle, which provides clear evidence for an increased understanding of milk fatty acid synthesis and enhances opportunities to improve milk-fat composition in dairy cattle.

Li C ，Sun D ，Zhang S ，Liu L ，Alim MA ，Zhang Q ... -  《-》

Associations of acetyl-coenzyme A carboxylase α, stearoyl-coenzyme A desaturase, and lipoprotein lipase genes with dairy traits in Alpine goats.

Milk yield and composition are of great economic importance for the dairy goat industry. The identification of genes associated with phenotypic differences for these traits could allow for the implementation of gene-assisted selection programs in goats. Associations between polymorphisms at 3 candidate genes and milk production traits in Alpine goats farmed in Italy were investigated in the present research. Considered genes were acetyl-coenzyme A carboxylase α (ACACA), the major regulatory enzyme of fatty acid biosynthesis; stearoyl-coenzyme A desaturase (SCD), involved in the biosynthesis of monounsaturated fatty acids in the mammary gland; and lipoprotein lipase (LPL), which plays a central role in plasma triglyceride metabolism. An approach somewhat similar to the granddaughter design for detecting quantitative trait loci in dairy cattle was followed. Effects of genotypes of a sample of 59 Alpine bucks on phenotypes of their 946 daughters raised in 75 flocks were investigated. Data comprised 13,331 daily records for milk yields (L/d), fat and protein yields (kg/d), and fat and protein contents (%) of 2,200 lactations. Population genetics parameters were calculated and associations between milk production traits and 10 single nucleotide polymorphisms (SNP) at the 3 genes were tested. Two markers at the ACACA, 1 for the SCD and 1 at the LPL locus, deviated significantly from the Hardy-Weinberg equilibrium, with an observed heterozygosity lower than expected. Flock, age of the goat, kidding season, and stage of lactation affected all traits considered, except fat percentage. Three SNP were found to be significantly associated with milk production traits. The SNP located on the ACACA gene showed an effect on milk yield, with daughters of TT bucks having an average test-day milk yield of about 0.3 to 0.25 L/d lower than the other 2 genotypes. The marker on the LPL locus was highly associated with milk yield, with the largest values for CC daughters (about 0.50L more than GG). The TGT deletion located on the untranslated region of the SCD gene showed significant effects on average milk and protein yields. The homozygote-deleted genotype had values about 0.5 L/d and 16 g/d lower for milk and protein daily yield, respectively, compared with the TGT/TGT genotype. Differences between genotypes were quite constant across most of the lactation. Associations found in the present study, which should be tested in a larger sample, especially for those markers that show rare genotypes, may offer useful indications for the genetic improvement of dairy traits in goats.

Crepaldi P ，Nicoloso L ，Coizet B ，Milanesi E ，Pagnacco G ，Fresi P ，Dimauro C ，Macciotta NP ... -  《-》

Association between a polymorphism at the stearoyl CoA desaturase locus and milk production traits in Italian Holsteins.

Associations between stearoyl-CoA desaturase (SCD) gene polymorphisms and milk production traits (milk, fat, and protein yields, fat and protein contents, somatic cell score) were investigated on a sample of 701 lactations of 313 Italian Holsteins. Test-day records (5,097) were analyzed with a mixed linear model that included the fixed effects of herd, date of test, parity, genotype at the SCD locus, and lactation interval nested within SCD genotype, and the random effect of cow. An effect of the SCD genotype on milk and protein yields was detected, with VV cows producing more milk (about 2 kg/d) and protein (about 0.07 kg/d) compared with AA cows. The contribution of the SCD locus to the phenotypic variance of the 2 traits was about 0.015. These results suggest a possible use of the SCD locus in gene-assisted selection programs for the improvement of milk production traits in dairy cattle, although large-scale studies in different breeds are required.

Macciotta NP ，Mele M ，Conte G ，Serra A ，Cassandro M ，Dal Zotto R ，Borlino AC ，Pagnacco G ，Secchiari P ... -  《-》

Single Nucleotide Polymorphisms of NUCB2 and their Genetic Associations with Milk Production Traits in Dairy Cows.

We previously used the RNA sequencing technique to detect the hepatic transcriptome of Chinese Holstein cows among the dry period, early lactation, and peak of lactation, and implied that the nucleobindin 2 () gene might be associated with milk production traits due to its expression being significantly increased in early lactation or peak of lactation as compared to dry period ( value < 0.05). Hence, in this study, we detected the single nucleotide polymorphisms (SNPs) of and analyzed their genetic associations with milk yield, fat yield, fat percentage, protein yield, and protein percentage. We re-sequenced the entire coding and 2000 bp of 5' and 3' flanking regions of by pooled sequencing, and identified ten SNPs, including one in 5' flanking region, two in 3' untranslated region (UTR), and seven in 3' flanking region. The single-SNP association analysis results showed that the ten SNPs were significantly associated with milk yield, fat yield, fat percentage, protein yield, or protein percentage in the first or second lactation ( values <= 1 × 10 and 0.05). In addition, we estimated the linkage disequilibrium (LD) of the ten SNPs by Haploview 4.2, and found that the SNPs were highly linked in one haplotype block (D' = 0.98-1.00), and the block was also significantly associated with at least one milk traits in the two lactations ( values: 0.0002-0.047). Further, we predicted the changes of transcription factor binding sites (TFBSs) that are caused by the SNPs in the 5' flanking region of , and considered that g.35735477C>T might affect the expression of by changing the TFBSs for ETS transcription factor 3 (ELF3), caudal type homeobox 2 (CDX2), mammalian C-type LTR TATA box (VTATA), nuclear factor of activated T-cells (NFAT), and v-ets erythroblastosis virus E26 oncogene homolog (ERG) (matrix similarity threshold, MST > 0.85). However, the further study should be performed to verify the regulatory mechanisms of and its polymorphisms on milk traits. Our findings first revealed the genetic effects of on the milk traits in dairy cows, and suggested that the significant SNPs could be used in genomic selection to improve the accuracy of selection for dairy cattle breeding.

Han B ，Yuan Y ，Li Y ，Liu L ，Sun D ... -  《Genes》